Open Access Method

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

Reuben Thomas1, Julia M Gohlke1, Geffrey F Stopper2, Frederick M Parham1 and Christopher J Portier1*

Author Affiliations

1 Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, RTP, NC 27709, USA

2 Department of Biology, Sacred Heart University, Fairfield, CT 06825, USA

For all author emails, please log on.

Genome Biology 2009, 10:R44  doi:10.1186/gb-2009-10-4-r44

Published: 24 April 2009

Additional files

Additional data file 1:

Estimation of P-values and additional tables of results.

Format: DOC Size: 101KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 2:

The nodes of this network are pathways while the edges indicate the transfer of signal or material between the pathways.

Format: PNG Size: 512KB Download file

Open Data

Additional data file 3:

(a) Sensitivity versus '1 - specificity' of enriched pathways that are predictive of survival from lung cancer for the six methods: SEPEA_NT1, SEPEA_NT1*, SEPEA_NT2, SEPEA_NT3, GSEA and maxmean. SEPEA_NT1* is the same analysis as in SEPEA_NT1 except that the pathway network information was not used. (b) Positive predictive power (ppp) versus negative predictive power (npp) for the same data and using the same methods of analysis as in (a).

Format: EPS Size: 16KB Download file

Open Data

Additional data file 4:

P-values for KEGG [44] pathways after cyclopamine treatment of developing X. laevis, designed to inhibit SHH signaling, using microarray data from GEO [45] [GEO:GSE8293]. P-values were obtained using SEPEA_NT1, SEPEA_NT2, SEPEA_NT3, GSEA and maxmean analyses with 1,000 randomizations to compute significance.

Format: XLS Size: 50KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data